title: TF ChIP-seq from heart right ventricle (ENCSR089NBS)

summary:
CTCF TF ChIP-seq on heart right ventricle tissue male adult (73 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from activated T-helper 2 cell (ENCSR193QAG)

status: Public on Nov 04 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Control Mint-ChIP-seq on activated T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4 , anti-CD3 and anti-CD28 coated beads

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCSR092CNB)

type: Expression profiling by high throughput sequencing

summary:
polyA plus RNA-seq of IgD-negative memory B cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCSR367WVH)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from activated T-cell (ENCSR092SRS)


title: Histone ChIP-seq from colonic mucosa (ENCSR078LIZ)

summary:
H3K27ac ChIP-seq on colonic mucosa tissue female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR368KWU)

summary:
H3K27me3 ChIP-seq on heart right ventricle tissue male adult (66 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from pancreas (ENCSR368EPJ)

summary:
H3K9me3 ChIP-seq on pancreas tissue female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from mesothelial cell of epicardium (ENCSR191AZW)

summary:
H3K36me3 Mint-ChIP-seq on mesothelial cell of epicardium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from gastrocnemius (ENCSR367VMG)

summary:
gastrocnemius B6Cast F1 PND4 Female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR367RUF)

summary:
H3K4me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from activated regulatory T cell (ENCSR364HOR)


title: DNase-seq from adrenal gland (ENCSR365LKY)


title: Histone ChIP-seq from lower lobe of left lung (ENCSR368APT)

summary:
H3K9me3 ChIP-seq on lower lobe of left lung tissue female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from A549 (ENCSR365RFY)

summary:
ChIP-seq on human A549

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from regulatory T cell (ENCSR075MGD)


title: TF ChIP-seq from HepG2 (ENCSR363XHT)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: WGBS from cerebral cortex (ENCSR277BIL)

type: Methylation profiling by high throughput sequencing

summary:
Whole genome bisulfite-seq on 8 week adult mouse cerebral cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from left cerebral cortex (ENCSR074RIB)


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR074OSI)


title: total RNA-seq from heart (ENCSR363LZO)

summary:
B6Cast F1 PND36 Male heart

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR072GKC)

summary:
H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (82 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from naive B cell (ENCSR363BVN)

summary:
polyA plus RNA-seq of naive B cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCSR069ZFG)

summary:
Control Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (35 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR073BPG)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from cerebellum (ENCSR361FXJ)


title: microRNA-seq from adrenal gland (ENCSR359KCJ)

type: Non-coding RNA profiling by high throughput sequencing

summary:
RNA Evaluation mouse PND4 male adrenals microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCSR070IHF)

summary:
Control Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from motor neuron (ENCSR358AOC)

summary:
H3K4me1 ChIP-seq on human motor neuron

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from left ventricle myocardium inferior (ENCSR068HEE)

summary:
CTCF ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR067BGS)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue male adult (87 years) with Alzheimer's disease, Cognitive impairment

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from T-helper 2 cell (ENCSR066VKF)

summary:
H3K4me1 Mint-ChIP-seq on T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCSR065QAA)

summary:
H3K4me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from activated T-helper 1 cell (ENCSR188HBL)

summary:
Control Mint-ChIP-seq on activated T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from WTC11 (ENCSR356QPN)

summary:
H3K36me3 Mint-ChIP-seq on WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from head of caudate nucleus (ENCSR355PNF)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from T-helper 1 cell (ENCSR352UAU)

summary:
Control Mint-ChIP-seq on T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCSR186VDY)

summary:
Control Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: BruUV-seq from IMR-90 (ENCSR351BRO)


title: DNase-seq from head of caudate nucleus (ENCSR274FZD)


title: ATAC-seq from motor neuron (ENCSR065CER)


title: TF ChIP-seq from heart left ventricle (ENCSR350NBQ)

summary:
CTCF TF ChIP-seq on heart left ventricle tissue male adult (54 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from adrenal gland (ENCSR188XCX)

summary:
CTCF ChIP-seq on adrenal gland tissue female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from adrenal gland (ENCSR270SAI)

summary:
adrenal gland_B6Cast F1 PND36_Female 03_ENC4_cDNA456

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR062JAC)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from heart left ventricle (ENCSR061EXX)

summary:
Control ChIP-seq on heart left ventricle tissue male adult (66 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from endodermal cell (ENCSR349NAK)

summary:
H3K27ac Mint-ChIP-seq on endodermal cell originated from H1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: GM DNase-seq from K562 (ENCSR272KNE)

summary:
TALEN-mediated homozygous DHS deletion in K562.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from HCT116 (ENCSR182JAI)


title: TF ChIP-seq from middle frontal area 46 (ENCSR270KFY)


title: Histone ChIP-seq from middle frontal area 46 (ENCSR181OHF)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from mesothelial cell of epicardium (ENCSR268SLH)

summary:
Control Mint-ChIP-seq on mesothelial cell of epicardium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from gastrocnemius (ENCSR515OMM)

summary:
RNA Evaluation mouse PND10 male gastrocnemius microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR267CTW)

summary:
H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (83 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from endodermal cell (ENCSR266XAJ)

summary:
LRGASP_H1_endo

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from IgD-negative memory B cell (ENCSR348YVF)

summary:
polyA plus RNA-seq of IgD-negative memory B cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from lung (ENCSR059VAQ)


title: polyA plus RNA-seq from CD4-positive, alpha-beta memory T cell (ENCSR266LHQ)

summary:
polyA plus RNA-seq of CD4-positive, alpha-beta memory T cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from spleen (ENCSR266CJT)

summary:
CTCF ChIP-seq on spleen tissue female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from posterior cingulate gyrus (ENCSR059ETS)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from CD14-positive monocyte (ENCSR264LON)

summary:
polyA plus RNA-seq of CD14-positive monocyte with multiple sclerosis.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from HCT116 (ENCSR345XUN)


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR060NQN)

summary:
H3K27me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from heart left ventricle (ENCSR261PLD)

summary:
Control ChIP-seq on heart left ventricle tissue female adult (56 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR260TLP)

summary:
H3K4me1 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (30 years) treated with anti-CD3 and anti-CD28 coated beads

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR181ELQ)

summary:
eGFP-OVOL2 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from activated CD8-positive, alpha-beta T cell (ENCSR264VJN)

summary:
CD8+ T cells, activated day 2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from thymus (ENCSR179HEN)


title: TF ChIP-seq from middle frontal area 46 (ENCSR059KXR)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from HCT116 (ENCSR059BAR)


title: ATAC-seq from activated regulatory T cell (ENCSR261PWP)


title: Control ChIP-seq from middle frontal area 46 (ENCSR058XPK)

summary:
Control ChIP-seq on middle frontal area 46 tissue male adult (83 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR178NOK)

summary:
H3K4me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR342KXD)

summary:
H3K27ac ChIP-seq on heart right ventricle tissue male adult (43 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from HCT116 (ENCSR260SWI)


title: Histone ChIP-seq from heart right ventricle (ENCSR056GGE)

summary:
H3K4me1 ChIP-seq on heart right ventricle tissue male adult (69 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta memory T cell (ENCSR177XCG)

summary:
memory CD4+ T cell (CD45RO+CCR7+/-)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from colonic mucosa (ENCSR340ARM)

summary:
H3K27me3 ChIP-seq on colonic mucosa tissue female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR178KWE)

summary:
H3K4me3 ChIP-seq on heart right ventricle tissue male adult (43 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR339TAQ)

summary:
H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (87 years) with Alzheimer's disease, Cognitive impairment

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from layer of hippocampus (ENCSR338WMA)

summary:
hippocampus B6CastF1 PND25 female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from adrenal gland (ENCSR335XKT)

summary:
RNA Evaluation mouse PND36 male adrenals microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR259KUF)

summary:
H3K36me3 ChIP-seq on heart right ventricle tissue male adult (73 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from effector memory CD4-positive, alpha-beta T cell (ENCSR255OLH)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from activated CD4 positive, naive alpha-beta T cell (ENCSR174SUM)


title: Control ChIP-seq from heart left ventricle (ENCSR170MJE)

summary:
Control ChIP-seq on heart left ventricle tissue male adult (73 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from heart right ventricle (ENCSR049JKQ)

summary:
Control ChIP-seq on heart right ventricle tissue female adult (59 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCSR053BET)

summary:
H3K36me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCSR338WIW)

summary:
polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR051QLZ)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (81 years) with Cognitive impairment

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR048OAV)

summary:
H3K9me3 ChIP-seq on heart left ventricle tissue male adult (54 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from T-cell (ENCSR258RSH)


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCSR171BDF)

summary:
H3K9me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR257VEO)

summary:
H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (82 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from activated effector memory CD8-positive, alpha-beta T cell (ENCSR335LHS)


title: WGBS from olfactory bulb (ENCSR334YHO)

summary:
Whole genome bisulfite-seq on 8 week adult mouse olfactory bulb

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR243BPI)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR042SVA)

summary:
polyA plus RNA-seq of naive thymus-derived CD4-positive, alpha-beta T cell with multiple sclerosis.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from natural killer cell (ENCSR044ATC)


title: microRNA-seq from adrenal gland (ENCSR049ABM)

summary:
RNA Evaluation mouse PND25 male adrenals microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR248FZA)

summary:
Control Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from WTC11 (ENCSR049LUW)

summary:
ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR244KEW)

summary:
CTCF ChIP-seq on middle frontal area 46 tissue female adult (88 years) with mild cognitive impairment

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR168WMQ)

summary:
H3K27ac Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from left cerebral cortex (ENCSR248KDJ)

summary:
B6Cast F1 PND25 Female L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR174GMQ)

summary:
H3K27ac ChIP-seq on heart right ventricle tissue male adult (69 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from brain (ENCSR049SVH)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from immature natural killer cell (ENCSR039JPA)

summary:
polyA plus RNA-seq of immature natural killer cell with multiple sclerosis.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR038QZA)


title: DNase-seq from head of caudate nucleus (ENCSR042DVU)


title: DNase-seq from activated regulatory T cell (ENCSR242CLA)


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR168LSG)

summary:
H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from heart left ventricle (ENCSR040TRJ)

summary:
Control ChIP-seq on heart left ventricle tissue male adult (54 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from heart (ENCSR168HGB)


title: TF ChIP-seq from SK-N-SH (ENCSR036THH)

summary:
eGFP-BACH2 ChIP-seq on human SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: BruUV-seq from HCT116 (ENCSR037CVT)


title: DNase-seq from cerebellum (ENCSR240XYH)


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR167NUS)

summary:
polyA plus RNA-seq of naive thymus-derived CD8-positive, alpha-beta T cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from activated CD8-positive, alpha-beta memory T cell (ENCSR240JQW)

summary:
Memory CD8+ cell, activated Day 7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCSR236OFL)

summary:
H3K4me3 Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR032XLY)

summary:
H3K36me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell..

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from head of caudate nucleus (ENCSR233DFT)


title: Control ChIP-seq from middle frontal area 46 (ENCSR237ZMF)

summary:
Control ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from gastrocnemius (ENCSR238FNF)

summary:
:gastrocnemius B6Cast F1 PND10 Female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR033XWU)

summary:
CD4+ T cells (CD3+CD4+)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR165LOY)

summary:
H3K36me3 ChIP-seq on heart left ventricle tissue male adult (73 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR231CZR)

summary:
eGFP-SOX15 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR159RNX)

summary:
H3K9me3 ChIP-seq on heart right ventricle tissue female adult (59 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated T-cell (ENCSR163WUL)

summary:
H3K9me3 Mint-ChIP-seq on activated T-cell male adult (42 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours..

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCSR030MGY)

summary:
H3K27me3 Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR165BJO)

summary:
H3K27me3 ChIP-seq on heart left ventricle tissue male adult (43 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from regulatory T cell (ENCSR159GFS)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from effector memory CD8-positive, alpha-beta T cell (ENCSR232FAS)


title: TF ChIP-seq from WTC11 (ENCSR027BEE)

summary:
eGFP-CDX4 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from adrenal gland (ENCSR158WTT)

summary:
adrenal gland_B6Cast F1 PND4_Female 03_ENC4_cDNA440

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from head of caudate nucleus (ENCSR161ZGA)


title: DNase-seq from central memory CD8-positive, alpha-beta T cell (ENCSR160VHJ)


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR159UIB)

summary:
polyA plus RNA-seq of naive thymus-derived CD8-positive, alpha-beta T cell with multiple sclerosis.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from kidney (ENCSR023EDS)


title: DNase-seq from kidney (ENCSR162TZA)


title: DNase-seq from adrenal gland (ENCSR021YHN)


title: total RNA-seq from activated CD4 positive, naive alpha-beta T cell (ENCSR152FDX)

summary:
Naïve CD4+ T cell, activated Day 7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCSR151FXS)

summary:
CD8+ T cells (CD3+CD8+)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from cerebellum (ENCSR026MFT)


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR152BBF)

summary:
polyA plus RNA-seq of naive thymus-derived CD8-positive, alpha-beta T cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR154NYM)


title: total RNA-seq from HFFc6 (ENCSR146ZSP)

summary:
Clonal line 6 derived from hTert immortalized HFF 600 ng

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mammary epithelial cell (ENCSR020YQE)

summary:
HMEC for bru-seq comparison

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from thymus (ENCSR021IRX)


title: DNase-seq from lung (ENCSR224ZGJ)


title: Mint-ChIP-seq from WTC11 (ENCSR146DPQ)

summary:
H3K27ac Mint-ChIP-seq on WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from adrenal gland (ENCSR018FOQ)

summary:
RNA Evaluation mouse PND14 female adrenals microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCSR226PSA)

summary:
H3K36me3 Mint-ChIP-seq on activated CD4 positive, naive alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from heart right ventricle (ENCSR145RXI)

summary:
Control ChIP-seq on heart right ventricle tissue male adult (73 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from heart (ENCSR145TJB)


title: polyA plus RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCSR230KVL)


title: Mint-ChIP-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR012DUX)

summary:
H3K36me3 Mint-ChIP-seq on activated CD8-positive, naive alpha-beta T cell male adult (30 years) treated with anti-CD3 and anti-CD28 coated beads

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from SK-N-SH (ENCSR219GUP)

summary:
eGFP-ZC3H10 ChIP-seq on human SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCSR144ABJ)

summary:
H3K4me3 Mint-ChIP-seq on CD8-positive naive resting alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from activated T-cell (ENCSR137UJW)

summary:
H3K4me3 Mint-ChIP-seq on activated T-cell male adult (42 years) treated with 50 U/mL Interleukin-2 for 4 hours, anti-CD3 and anti-CD28 coated beads for 4 hours..

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Bru-seq from PC-9 (ENCSR223GHJ)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from neural crest cell (ENCSR012MIG)

summary:
H3K36me3 Mint-ChIP-seq on neural crest cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from left cerebral cortex (ENCSR219ZXZ)

summary:
B6Cast F1 PND 2 months Female L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCSR009ZRH)

summary:
H3K27me3 Mint-ChIP-seq of IgD-negative memory B cell originated from IgD-negative memory B cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from adrenal gland (ENCSR007NGM)

summary:
adrenal gland_B6Cast F1 PND 2 months_Male 03_ENC4_cDNA458

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from head of caudate nucleus (ENCSR010SZN)


title: microRNA-seq from adrenal gland (ENCSR138BVH)

summary:
RNA Evaluation mouse PND14 male adrenals microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from neural crest cell (ENCSR219DIX)

summary:
H3K27me3 Mint-ChIP-seq on neural crest cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from CD8-positive, alpha-beta memory T cell (ENCSR007OKF)

summary:
polyA plus RNA-seq of CD8-positive, alpha-beta memory T cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from HCT116 (ENCSR135OML)


title: Histone ChIP-seq from heart left ventricle (ENCSR135GZX)

summary:
H3K4me3 ChIP-seq on heart left ventricle tissue male adult (43 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from T-helper 1 cell (ENCSR005ZRX)

summary:
H3K36me3 Mint-ChIP-seq on T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR215QQE)

summary:
H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Cognitive impairment.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from gastrocnemius (ENCSR133LMN)

summary:
gastrocnemius B6Cast F1 PND10 Male

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RAMPAGE from foreskin keratinocyte (ENCSR215UXA)

summary:
RAMPAGE on primary keratinocytes in day 1.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from motor neuron (ENCSR131HOY)


title: Mint-ChIP-seq from activated T-helper 2 cell (ENCSR002RFV)

summary:
H3K27ac Mint-ChIP-seq on activated T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4 , anti-CD3 and anti-CD28 coated beads

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR001ZXO)

summary:
H3K27me3 ChIP-seq on heart right ventricle tissue male adult (69 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: WGBS from thymus (ENCSR001MFH)

summary:
Whole genome bisulfite-seq on 8 week adult mouse thymus

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR130XNJ)

summary:
H3K4me1 ChIP-seq on heart left ventricle tissue male adult (61 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from T-helper 1 cell (ENCSR005QYU)

summary:
H3K27me3 Mint-ChIP-seq on T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR130NZQ)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from layer of hippocampus (ENCSR128FBT)

summary:
hippocampus B6CastF1 PND14 3x female

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR122KBB)

summary:
H3K36me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from heart (ENCSR121JAB)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: WGBS from small intestine (ENCSR211VXF)

summary:
Whole genome bisulfite-seq on 8 week adult mouse small intestine

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from T-helper 1 cell (ENCSR128HUJ)

summary:
H3K27ac Mint-ChIP-seq on T-helper 1 cell male adult (35 years) treated with 1 ?g/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from spleen (ENCSR119AVG)

summary:
Control ChIP-seq on spleen tissue female adult (61 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR216YPQ)

summary:
H3K4me3 ChIP-seq on heart right ventricle tissue male adult (73 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCSR332WFE)

summary:
H3K27me3 Mint-ChIP-seq on progenitor cell of endocrine pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from pancreas (ENCSR133RZO)

summary:
H3K27me3 ChIP-seq on pancreas tissue female child (16 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from heart right ventricle (ENCSR004ACG)

summary:
RNA Evaluation human tissue W73 heart right ventricle microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RAMPAGE from foreskin keratinocyte (ENCSR215PII)

summary:
RAMPAGE on primary keratinocytes in day 4.5 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from head of caudate nucleus (ENCSR002IHL)


title: Histone ChIP-seq from mucosa of descending colon (ENCSR001UVQ)

summary:
H3K36me3 ChIP-seq on mucosa of descending colon tissue male adult (40 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: BruUV-seq from PC-3 (ENCSR331BIC)


title: Mint-ChIP-seq from mesothelial cell of epicardium (ENCSR213GNK)

summary:
H3K4me1 Mint-ChIP-seq on mesothelial cell of epicardium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR214NBT)

summary:
polyA plus RNA-seq of CD4-positive, CD25-positive, alpha-beta regulatory T cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR123OMJ)

summary:
H3K4me3 ChIP-seq on heart left ventricle tissue male adult (66 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR124IGC)

summary:
H3K4me1 Mint-ChIP-seq on CD4-positive, CD25-positive, alpha-beta regulatory T cell with multiple sclerosis..

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Bru-seq from OCI-LY7 (ENCSR121MLV)


title: Mint-ChIP-seq from endodermal cell (ENCSR121HJH)

summary:
H3K36me3 Mint-ChIP-seq on endodermal cell originated from H1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from HCT116 (ENCSR328JGW)


title: polyA plus RNA-seq from inflammation-experienced regulatory T-cells (ENCSR128KAW)


title: Histone ChIP-seq from inflammation-experienced regulatory T-cells (ENCSR118TPX)


title: BruUV-seq from OCI-LY7 (ENCSR114UOQ)


title: ATAC-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR326ESM)


title: DNase-seq from brain (ENCSR330JXM)


title: total RNA-seq from layer of hippocampus (ENCSR330DDD)

summary:
hippocampus B6Cast F1 2 months male

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from chondrocyte (ENCSR117SLI)

summary:
H3K4me1 Mint-ChIP-seq on chondrocyte.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from activated T-helper 17 cell (ENCSR115OIV)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: GM DNase-seq from K562 (ENCSR324UCN)


title: Histone ChIP-seq from middle frontal area 46 (ENCSR116MKX)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (88 years) with mild cognitive impairment

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from kidney (ENCSR113CGA)


title: Mint-ChIP-seq from endodermal cell (ENCSR322YYC)

summary:
H3K4me1 Mint-ChIP-seq on endodermal cell originated from H1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from heart right ventricle (ENCSR323ZAP)

summary:
CTCF TF ChIP-seq on heart right ventricle tissue female adult (56 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from T-helper 2 cell (ENCSR327ZJA)

summary:
H3K9me3 Mint-ChIP-seq on T-helper 2 cell male adult (35 years) treated with 5 ?g/mL Interferon-gamma antibody , 100 ng/mL Interleukin-4

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from left cerebral cortex (ENCSR321WYK)

summary:
B6Cast F1 PND10 Female L. cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR326YRW)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with mild cognitive impairment.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from thymus (ENCSR315TVO)


title: Mint-ChIP-seq from chondrocyte (ENCSR115EBL)

summary:
H3K36me3 Mint-ChIP-seq on chondrocyte

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Identification of known and novel long non-coding RNAs potentially responsible for the effects of BMD GWAS loci

city: CHARLOTTESVILLE

first: Abdullah

last: Abood

state: VA

address: OMS, Room 3817B

institute: University of Virginia

summary: Osteoporosis, characterized by low bone mineral density (BMD), is the most common complex disease affecting bone and constitutes a major societal health problem. Genome-wide association studies (GWASs) have identified over 1100 associations influencing BMD. It has been shown that perturbations to long non-coding RNAs (lncRNAs) influence BMD and the activities of bone cells; however, the extent to which lncRNAs are involved in the genetic regulation of BMD is unknown. Here, we combined the analysis of allelic imbalance (AI) in human acetabular bone fragments with a transcriptome-wide association study (TWAS) and expression quantitative trait loci (eQTL) colocalization analysis using data from the Genotype-Tissue Expression (GTEx) project to identify lncRNAs potentially responsible for GWAS associations. We identified 27 lncRNAs in bone that are located in proximity to a BMD GWAS association and harbor SNPs demonstrating AI. Using GTEx data we identified an additional 31 lncRNAs whose expression was associated (FDR correction<0.05) with BMD through TWAS and had a colocalizing eQTL (regional colocalization probability (RCP)>0.1). The 58 lncRNAs are located in 43 BMD associations. To further support a causal role for the identified lncRNAs, we show that 23 of the 58 lncRNAs are differentially expressed as a function of osteoblast differentiation. Our approach identifies lncRNAs that are potentially responsible for BMD GWAS associations and suggest that lncRNAs play a role in the genetics of osteoporosis.

overall_design: Acetabular reaming from 17 Boston Medical Center (BMC) patients (ages 43-80 year) undergoing elective hip arthroplasty were collected: 12 Females and 5 Males; 8 Black, 8 White, and 1 Hispanic

first: Charles

last: Farber


title: RNA-seq of human whole-blood samples before and after the administration of recombinant human erythropoietin

city: Eastbourne

first: Guan

last: Wang

address: 30 Carlisle Rd

department: School of Sport and Health Sciences

country: United Kingdom

institute: University of Brighton

summary: As part of cross-platform comparisons of microarray and RNA-seq, the current experiment using the Illumina NextSeq 500 and MGI DNBSEQ-G400RS aimed to quantify gene-level expression in subjects administered recombinant human erythropoietin over a 10-week protocol for the identification of gene signatures of blood doping. These results were compared to results obtained from other gene expression quantification platforms using the same experimental cohort, including the Illumina HumanHT-12v4 Expression BeadChips (archived in ArrayExpress; E-MTAB-2874) and Affymetrix Human Transcriptome Array 2.0 (archived in ArrayExpress; E-MTAB-11080).

overall_design: Whole blood samples of 10 endurance-trained Caucasian males at sea level from Glasgow, Scotland were subject to analysis in the current study. The 10 subjects were part of 18 subjects previously analysed on the Illumina HumanHT-12v4 Expression BeadChip (E-MTAB-2874). Briefly, they underwent 4-week 50 IU/kg body mass of recombinant human erythropoietin (rHuEPO) injections every 2 days. Daily oral iron supplementation (100 mg of elemental iron, ferrous sulphate tablets, Almus, Barnstable, UK) was given during the 4 weeks of rHuEPO administration. Here, whole blood samples collected at baseline (Base1 and Base2), during the rHuEPO administration (2 days and 2 weeks following the 1st injection; EPO3 and EPO4) and for 2 weeks after the rHuEPO administration (Post7) were analysed on the Illumina NextSeq 500 and MGI DNBSEQ-G400RS.

first: Traci

last: Kitaoka

first: Ali

last: Crawford

first: Qian

last: Mao

first: Andrew

last: Hesketh

first: Fergus

middle: M

last: Guppy

first: Garrett

middle: I

last: Ash

first: Jason

last: Liu

first: Mark

middle: B

last: Gerstein

first: Yannis

middle: P

last: Pitsiladis


title: Mint-ChIP-seq from progenitor cell of endocrine pancreas (ENCSR112DVZ)

summary:
H3K4me1 Mint-ChIP-seq on progenitor cell of endocrine pancreas

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RAMPAGE from foreskin keratinocyte (ENCSR115BCB)

summary:
RAMPAGE on primary keratinocytes in day 6.0 of differentiation

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA plus RNA-seq from regulatory T cell (ENCSR323OER)


title: Mint-ChIP-seq from CD4-positive naive resting alpha-beta T cell (ENCSR324IEM)

summary:
H3K27ac Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (42 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: A novel meiosis-related lncRNA, Rbakdn, contributes to spermatogenesis by stabilizing Ptbp2

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

summary: Spermatocyte meiosis is the cornerstone of mammalian production. Thousands of long noncoding RNAs (lncRNAs) have been reported to be functional in various cellular processes, but the function of lncRNAs in meiosis remains largely unknown. Here, we profiled lncRNAs in spermatocytes at stage I of meiosis and identified a testis-specific lncRNA, Rbakdn, as a vital regulator of meiosis. Rbakdn is dynamically expressed during meiosis I, and Rbakdn knockdown inhibits meiosis in vitro. Furthermore, Rbakdn knockdown in testes in mice by intratesticular injection disturbs meiosis, reduces testicular volume, and increases apoptosis of spermatocytes, resulting in vacuolation of the seminiferous tubules. Rbakdn can bind to Ptbp2, an RNA-binding protein that is important in the regulation of the alternative splicing of many genes in spermatogenesis. Rbakdn knockdown leads to a decrease in Ptbp2 through the ubiquitination degradation pathway, indicating that Rbakdn maintains the stability of Ptbp2. In conclusion, our study identified an lncRNA, Rbakdn, with a crucial role in meiosis.

overall_design: RNA profiles of spermatogonia, preleptotene, leptotene/zygotene, and pachytene spermatocytes cells

first: Wensheng


title: Modeling of lung phenotype of Hermansky-Pudlak syndrome type I using patient-specific iPS cells

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Inhibiting Hh signaling in Gli1+ osteogenic progenitors alleviates TMJOA

city: Los Angeles

first: Jie

last: Lei

address: 2250 Alcazar Street, CSA 103

department: Ostrow School of Dentistry

institute: University of Southern California

summary: The goal of this study is to investigate the role of Gli1+ osteogenic progenitors in the development of TMJOA.

overall_design: Methods: mRNA profiles of  mice receiving sham or partial discectomy surgery were generated by deep sequencing, in triplicate, usingNextSeq500 High Output. The quality of RNA samples was determined using an Agilent 2100 Bioanalyzer and all samples for sequencing had RNA integrity numbers >6.


title: DNase-seq from activated CD8-positive, naive alpha-beta T cell (ENCSR114XWV)

first: ENCODE


title: DNase-seq from thymus (ENCSR322AIL)


title: RNA-seq of healthy and osteoarthritic menisci

city: Guangzhou

first: Zongrui

last: Jiang

state: Guangdong

address: No.58 of 2nd Zhongshan Road, Yuexiu District, Guangzhou, Guangdong

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: We report the application of RNA sequence on healthy and osteoarthritic degenerative meniscus. A total of 677 mRNAs were screened out. qRT-PCR further revealed consistent expression pattern.

overall_design: Examination of healthy and OA degenerative meniscus

first: Xue

last: Du

first: Weiming

last: Liao

first: Zhiqi

last: Zhang


title: Modeling of lung phenotype of Hermansky-Pudlak syndrome type I using patient-specific iPS cells (NaPi2Bhigh cells)

summary: We generated iPSCs from HPS1 patient-derived fibroblasts with bi-allelic c.1472_1487dup16 variant in HPS1 gene and their gene-corrected ones and differentiated them into alveolar epithelial cells in organoids for disease modeling of HPS1.

overall_design: HPS1 patient-specific iPSCs and their gene corrected ones were differentiated into NKX2-1 positive lung progenitor cells. NKX2-1 positive lung progenitor cells enriched by the surface expression of CPM were cocultured with human fetal lung fibroblasts to generate alveolar epithelial type 2 (AT2) cells. AT2 cells were passaged 3 times by the surface expression of NaPi2B and isolated with NaPi2B high expression.

first: Takahiro

last: Suezawa


title: whole transcriptome map of osteoarthritic meniscus with or without interleukin-1β stimulation

summary: We report the application of whole-transcriptome high throughput sequence on osteoarthritic degenerative meniscus with or without interleukin-1β stimulation. A total of 375 mRNAs, 15 miRNAs, 56 lncRNAs, and 90 circRNAs were significantly altered in the degenerative meniscus treated with IL-1β. qRT-PCR further revealed consistent expression pattern. More importantly, highly specific ceRNA networks regulated by lncRNA LOC107986251-miR-212-5p-SESN3 and hsa_circ_0018069-miR-147b-3p-TJP2 were identified during interleukin-induced meniscus degeneration.

overall_design: Examination of degenerative meniscus with or without interleukin-1β stimulation


title: Histone ChIP-seq from heart right ventricle (ENCSR324APQ)

last: DCC

summary:
H3K36me3 ChIP-seq on heart right ventricle tissue female adult (59 years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: CNOT6/6L-mediated mRNA Degradation in Ovarian Granulosa Cells is a Key Mechanism of Gonadotropin-triggered Follicle Development

city: Hangzhou

first: Xingxing

last: Dai

address: YuHangTang 866

institute: Life Sciences Institute

summary: CCR4-NOT deadenylase is a major regulator of mRNA turnover in eukaryotes. It contains 2 heterogeneous catalytic subunits encoded by Cnot7/8 and Cnot6/6l genes in vertebrates, respectively. The physiological function of each catalytic subunit was unclear due to potential gene redundancy in vivo. In this study Cnot6/6l double knockout mice were generated. These mice were viable and generally healthy, but females were infertile with irregular estrus cycle and poor ovarian responses to gonadotropins. Follicle-stimulating hormone (FSH) stimulated transcription and translation of mRNAs encoding CNOT6 and CNOT6L in ovarian granulosa cells through the activity of phosphoinositide 3-kinase signaling pathway. Results of transcriptome analyses indicated that FSH downregulated a large number of transcripts in granulosa cells during the transition from pre-antral to antral follicles in a CNOT6/6L-dependent manner. These two deadenylases functioned as key effectors of FSH in altering the developmental programs in granulosa cells and triggered clearance of specific transcripts in growing follicles, particularly those encoding repressing factors of granulosa cell proliferation and steroidogenesis. These results demonstrated that FSH modulates granulosa cells function by stimulating selective translational activation and degradation of existed mRNAs, in additional to inducing de novo gene transcription. Meanwhile, this study provides in vivo evidence that CCR4-NOTCNOT6/6L-mediated mRNA deadenylation is dispensable in most somatic cell types, but is essential for the female reproductive endocrine regulation.

overall_design: Examination of WT and CNOT6/6L-null transcriptome in Ovarian Granulosa Cells.

first: Xing

middle: X

first: Zhi

middle: Y

first: Yun

middle: W

last: Wu


title: Effects of aneurysmal low and supra-high wall shear stress on endothelial gene expression

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: Wall shear stress (WSS) is proposed to influence intracranial aneurysm growth and rupture. Physiological WSS in cerebral arteries is estimated around 20-30 dynes/cm2. The WSS typically observed in human IAs is close to 2 dynes/cm2 for wide-neck aneurysms with a slow recirculating flow and >70 dynes/cm2 in aneurysms with impinging “jet flow”. In this study, we investigated the effects of aneurysmal low and supra-high WSS on endothelial cells.

overall_design: Primary porcine aortic endothelial cells (PECs) used in this study were cultured in DMEM medium supplemented with 10% fetal calf serum and 100 g/mL heparin. For flow experiments, cells were seeded on 1% gelatin coated Ibidi chambers. For low shear stress experiments (2 dynes/cm2), cells were seeded at 30.000 cells per channel in Ibidi μ-Slide VI 0.4. For supra-high shear stress experiments (80 dynes/cm2) cells were seeded at 100.000 cells per channel in Ibidi μ-Slide I 0.2 Luer. The different laminar shear stress conditions were applied for 48h using an Ibidi flow system. To allow comparison between low and physiological (30 dynes/cm2) shear stress, and between supra-high and physiological shear stress, experiments at 30 dynes/cm2 were performed either in Ibidi μ-Slides VI 0.4 (condition named as 302 dynes/cm2) or in Ibidi μ-Slides I 0.2 Luer (condition named as 3080 dynes/cm2), respectively.

first: Sandrine

last: Morel

first: Mannekomba

middle: R

last: Diagbouga

first: Brenda

last: Kwak


title: Gene expression in Parkinson modeled mouse substantia nigra pars compacta at single cell resolution

status: Public on Nov 03 2021

first: Desmond

middle: J

last: Smith

address: 650 Charles E Young Drive South

institute: UCLA

summary: Strong evidence in human populations indicates that pesticide exposure increases the risk of Parkinson's disease . However, to date there has no study investigating the role of genetic pathways for pesticide induced PD at cellular resolution. We used single cell RNA sequencing to provide fine-grained information on the genetic pathways of Parkinson's disease caused by a combined regimen of maneb and paraquat. We investigated the substantia nigra pars compacta of control mice and mice treated with maneb and paraquat to identify changes in gene expression in cellular subpopulations such as neurons, glia and vascular cells. This work reveals how neuronal and non-neuronal cells interact in the context of a toxicologically and environmentally relevant model Parkinson's disease, while offering entry points to the design of new therapies.

overall_design: Two samples were analyzed, control and experimental.

first: Arshad

middle: H

last: Khan


title: Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells (Micro-C XL)

city: Seattle

first: Sarah

middle: G.

last: Swygert

state: WA

address: 1100 Fairview Avenue North MS A1-162

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

summary: Determining the conformation of chromatin in cells at the nucleosome level and its relationship to cellular processes has been a central challenge in biology. We show that in quiescent yeast, widespread transcriptional repression coincides with the local compaction of chromatin fibers into structures that are less condensed and more heteromorphic than canonical 30-nanometer forms. Acetylation or substitution of H4 tail residues decompacts fibers and leads to global transcriptional de-repression. Fiber decompaction also increases the rate of loop extrusion by condensin. These findings establish a role for H4 tail-dependent local chromatin fiber folding in regulating transcription and loop extrusion in cells. They also demonstrate the physiological relevance of canonical chromatin fiber folding mechanisms even in the absence of regular 30-nanometer structures.

overall_design: Examination of log and quiescent cells, including quiescent cells from strains with substitutions in the histone H4 tail basic patch and cells treated with the histone deacetylase inhibitor TSA, by Micro-C XL.

middle: G


title: Expression data from mouse liver tissue treated by PM2.5 and metformin for two weeks.

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
There is a lot of epidemiological evidence that PM2.5 causes liver disease, and metformin can alleviate these diseases.However, the precise mechanism  remains unclear.Our study defined the dynamic changes of the differentially expressed genes  related PM2.5 induced diseases, and provide basis for comprehensive understanding of the mechanism at the transcriptome level.
We investigated PM2.5 induced gene expression alteration associated with the development of liver injury by microarray in a ob/ob mouse model.

overall_design: Mice were euthanized after two weeks PM2.5 exposure. Total RNA was isolated with TRIzol (Invitrogen) from liver organs (n=5 per group) at each time point according to manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). On the GeneChip Mouse Genome 430 2.0 Array, over 45,000 probe sets analyze the expression level of over 39,000 transcripts and variants from over 34,000 well characterized mouse genes.

first: Lisen

last: Lin

first: Li

last: Tian


title: Modeling of lung phenotype of Hermansky-Pudlak syndrome type I using patient-specific iPS cells (SPC positive cells)

first: Shimpei

last: Gotoh

overall_design: Healty donor derived SPC-GFP reporter iPSCs (B2-3) were differentiated into NKX2-1 positive lung progenitor cells. NKX2-1 positive lung progenitor cells enriched by the surface expression of CPM were cocultured with human fetal lung fibroblasts to generate alveolar epithelial type 2 (AT2) cells. AT2 cells were passaged 2-3 times by the  expression of SPC-GFP.


title: Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells


title: Exogenous and Endogenous Sources of Serine Contribute to Colon Cancer Metabolism and Growth

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Serine is a non-essential amino acid that is generated by the sequential actions of phosphoglycerate dehydrogenase (PHGDH), phosphoserine aminotransferase (PSAT1) and phosphoserine phosphatase (PSPH). Increased serine biosynthesis occurs in several cancers and supports tumor growth. In addition to serine synthesis, exogenous serine is taken up by cells and can also fuel tumor growth. Interestingly, colon cancer cells increase expression of serine biosynthesis enzymes in the absence of exogenous serine, suggesting a compensatory adaptive response to reduced availability of serine. This study explored the relative contributions of exogenous and synthesized serine to colon cancer cell growth, metabolism and response to anti-cancer therapy.

overall_design: Human colorectal cancer cells containing empty vector were cultured in control or serine deficient media  and PSAT1 knockout cells were cultured in serine deficient medium for 24 hours and RNA seq analysis was carried out.

first: David

middle: C

last: Montrose

first: Miguel

last: Foronda

first: Suchandrima

last: Saha

first: Erin

last: McNally

first: Xi

middle: K

last: Zhou

first: Jan

last: Krumsiek

first: Olivier

last: Elemento

first: Rhonda

last: Yantiss

first: Qiuying

last: Chen

first: Steven

middle: S

last: Gross

first: Lorenzo

last: Galluzzi

first: Lukas

middle: E

last: Dow

first: Andrew

last: Dannenberg


title: Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells (ChIP-Seq)

first: Sarah

last: Swygert

overall_design: Examination of binding of histone H3, penta-acetylated histone H4 tail, Hho1, RNA Polymerase II subunit Rpb3, and condensin subunit Brn1 in log and quiescent cells with wildtype backgrounds, bearing various histone H4 mutations, or treated with the histone decetylase inhibitor TSA or the transcriptional inhibitor phenanthroline.


title: Genome-wide mapping of Cbx3/HP1g deposition in wild-type CD8+ effector T cells

city: Boston

first: To-Ha

last: Thai

state: MA

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: We report the application of Illumina Hi-Seq sequencing technology for high-throughput profiling of Cbx3/HP1g deposition in mammalian CD8+ effector T cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, genome-wide chromatin-state maps of mouse wt CD8+ effector T cells were generated. We find that Cbx3/HP1g negatively regulates the germinal center and high-affinity antibody responses in a CD8+ T-cell-dependent manner. CD8-restricted deletion of Cbx3/HP1g confers hightened effector and persistence capacity on CD8+ effector T cells. As a result, Cbx3/HP1g-deficient CD8+ effector T cells can efficiently control solid tumor growth in vairious mouse models (melanoma, ovarian and neuroblstoma).

overall_design: Examination of Cbx3/HP1g genome-wide deposition in mouse CD8+ effector T cells


title: Cadmium-mediated Pancreatic Islet Transcriptome Changes in Mice and Cultured Mouse Islets.

city: Chicago

first: Malek

last: El Muayed

state: IL

address: 303 E. Chicago Ave Tarry 15

department: Endocrinology, Metabolism, and Molecular Medicine

institute: Northwestern University Feinberg School of Medicine

summary: The purpose of the study are 1) to describe the islet transcriptome profile of cadmium-exposed mice to determine changes in systemic regulatory networks and 2) to describe the transcriptome profile of mouse islets exposed to cadmium in culture/ex vivo to determine gene changes as a direct consequence of cadmium exposure.

overall_design: Islet transcriptome profile following 6 and 18 weeks of Cadmium exposure in vivo in WT male mice and following 96 hours of cadmium exposure in isolated mouse islet culture.

first: Winifred

last: Wong

first: Janice

last: Wang

first: Matthew

last: Schipma

first: Xiaomin

last: Zhang

first: Joshua

last: Edwards

last: El-Muayed


title: miR548ai antagonism attenuates exosome-induced endothelial cell dysfunction

city: charlottesville

first: Xiujie

last: Xie

address: 409 Lane Rd MR4

institute: university of virginia

summary: We performed microarray profiling of microRNAs of dysfunctional human primary aortic SMCs induced by different cytokines (PDGF-BB, TGFβ1, TNFα, IL1β).

overall_design: We identified a group of microRNAs that were commonly upregulated in dysfunctional SMCs, which were induced by PDGF-BB, TGFβ1, TNFα, IL1β, respectively.

first: Lianwang

last: Guo

first: Craig

last: Kent


title: Exposure of Air-Liquid-Interface bronchial epithelial cells to whole birch pollen

city: Munich

first: Joana

last: Candeias

address: Biedersteinerstr. 29

department: Center Allergy and Environment (ZAUM)

country: Germany

institute: Technical University Munich & Helmholtz Center Munich

summary: Human BEAS-2B were exposed to whole birch pollen using a Pollen Sedimentation Chamber. The chamber was designed to be able to dose cells to dry whole pollen. The goal was to understand the reaction of human epithelial cells to a human real life pollen exposure.

overall_design: BEAS-2B, at Air-Liquid-Interface, were exposed to 10 mg whole birch pollen for different incubation times (10 min, 55 min, 6h50 min and 24h). The cells were seeded in 24mm Transwells 48hours before exposure and kept in air lift conditions 24h before start. Three replicates were performed for each incubation time. Effects of birch whole pollen were referenced against cells exposed to air.

first: Carsten

last: Schmidt-Weber

first: Jeroen

last: Buters


title: Transcriptome profiles of control and PIM1 over-expressing LNCaP cells in complete media

first: Michael

last: Garabedian

state: NY

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

summary: We used control and PIM1 over-expressing LNCaP cells to analyze the effect of PIM1 on gene expression. We find that PIM1 over-expression results in up- and down-regulation of different classes of genes, including increasing gene expression involved in extracellular matrix organization, cell adhesion, and cytokine signaling.

overall_design: Examination by RNA-seq in control (3 replicates) and PIM1 over-expressing (2 replicates) LNCaP cells.

first: Sophie

last: Ruff

first: Nikita

last: Vasiliyev

first: Evgeny

last: Nudler

first: Susan

last: Logan


title: Expression profile of Normal Breast Tissue in Brazilian women

city: Rio de Janeiro

first: Renata

last: Binato

state: Rio de Janeiro

address: Praça Cruz Vermelha 23/ 6 andar ala C

country: Brazil

institute: INCA

summary: Control samples used to performed gene expression comparison with breast cancer tissues. mRNA samples from normal breast tissue were amplified, labeled, and hybridized to the Affymetrix GeneChip Human Exon 1.0 ST array. After normalization and analysis of the microarray data using Partek® software (http://www.partek.com).

overall_design: We analyzed normal breast tissues from 4 healthy women tissues using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by AffymetrixExpression Console and analysed using Partek software

first: Carolina

last: Panis

first: Eliana

last: Abdelhay


title: PIM1 phosphorylation of the androgen receptor and 14-3-3 ζ coordinates their interaction and chromatin occupancy to regulate gene transcription in prostate cancer

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Cholesterol depletion increases expression of autophagy-related genes in mink lung Mv1Lu cells

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary:
Purpose: Employ next generation sequencing (NGS) to study the transcriptomic response to prolonged reduction in the cholesterol level, with emphasis on autophagy-related genes.
Methods:  Mv1Lu cells were subjected (or not; control) to cholesterol depletion (16 h, with lovastatin and mevalonate in the presence of lipoprotein deficient serum (LPDS), resulting in 30% reduction in the level of free cholesterol).  mRNA profiles were generated by deep sequencing, in triplicates, using Illumina NextSeq500. See methods and protocols for details regarding downstream bioinformatic analysis.
Results: Using an optimized data analysis workflow sequencing data from lung samples and identified that cholesterol depletion resulted in 2844 and 2822 genes with significantly increased or reduced expression, respectively. The set of differentially expressed genes was significantly enriched with functional annotations relating to cholesterol metabolic regulation and autophagy. These results were correlated with the upregulation of autophagy in biochemical studies.
Conclusions: Mild reduction in the cholesterol level leads to a highly significant increase in the expression of multiple autophagy-related genes. The autophagy genes whose expression was modified by cholesterol depletion were scattered onto multiple steps of the autophagy process, and suggested a mainly positive regulation of autophagy by statin treatment.

overall_design: Comparison between mRNA profiles of Mv1Lu cells treated (or not; control) by statin for 16 h to induce mild reduction in the free cholesterol level.

first: Keren

first: Noam

last: Shomron

first: Metsada

last: Pasmanik-Chor

first: Yoav

last: Henis

first: Marcelo

last: Ehrlich


title: Genome-wide maps of the androgen receptor, pS213 androgen receptor, and 14-3-3 ζ chromatin occupancy in control and PIM1 over-expressing LNCaP cells

summary: We used ChIP-seq to identify chromatin binding sites for AR, 14-3-3 ζ, and pS213 AR in the absence and presence of PIM1 over-expression. We find that, as expected, pS213 AR occupancy almost completely overlaps with total AR occupancy, and increases in the presence of PIM1 over-expression. Additionally, the majority of pS213 AR sites are co-occupied by 14-3-3 ζ. 14-3-3 ζ is a known AR co-activator, but this study definitively shows its co-occupancy on chromatin with AR and pS213 AR.

overall_design: Examination by ChIP-seq of AR, pS213 AR, and 14-3-3 ζ in control LNCaP and PIM1 over-expressing LNCaP cells.


title: Deletion of Abi3 gene locus exacerbates neuropathological features of Alzheimer’s disease in a mouse model of Aβ amyloidosis

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

summary: Recently, large-scale human genetics studies identified a rare coding variant in the ABI3 gene that is associated with an increased risk of late-onset Alzheimer’s disease (AD).  However, pathways by which ABI3 contributes to the pathogenesis of AD are unknown.  To address this critical question, we determined whether loss of ABI3 function affects  pathological features of AD, such as amyloid- (A) accumulation, inflammation, and  synaptic dysfunction, in the 5XFAD mouse model. We demonstrate that the deletion of  Abi3 locus significantly increases levels of soluble and insoluble A and amyloid plaques  and decreases microglia clustering around the plaques. Furthermore, long-term  potentiation is impaired in Abi3 knock-out (Abi3-/-) mice. Nanostring-based transcriptomic  analyses indicate that genes involved in microglial phagocytosis and immune response  pathways are dysregulated in Abi3-/-mice. Moreover, we identified dramatic changes in  microglia subpopulations in Abi3-/- mice using a single-cell RNA sequencing approach.  Taken together, our study provides the first in vivo functional evidence that loss of ABI3  function may increase the risk of developing AD by affecting A pathway and  neuroinflammation.

overall_design: Two male 9-month old 5XFAD mice and two male 9-month old 5XFAD;Abi3 KO mice were used.

first: Hande

last: Karahan

first: Daniel

last: Smith

first: Byungwook

last: Kim

first: Md

last: Al-Amin

first: Taylor

last: Pennington

first: Gonzalo

middle: V

last: du Prisco

first: Brianne

last: McCord

first: Peter

last: Lin

first: Yuxin

last: Li

first: Junmin

last: Peng

first: Adrian

middle: L

last: Oblak

first: Brady

last: Atwood

first: Jungsu


title: Hepatic Lysosomal Acid Lipase Overexpression Worsens Hepatic Inflammation in Mice Fed a Western Diet

city: Minneapolis

first: Douglas

last: Mashek

state: MINNESOTA

address: 321 Church St. SE, Suite 6-155

institute: University of Minnesota

summary: Non-alcoholic fatty liver disease (NAFLD) is characterized by the accumulation of lipid droplets (LD) in hepatocytes. NAFLD development and progression is associated with an increase in hepatic cholesterol and decreased autophagy and lipophagy flux. Previous studies have shown that the expression of lysosomal acid lipase (gene=LIPA, protein=LAL), which can hydrolyze both triglyceride and cholesteryl esters, is inversely correlated with the severity of NAFLD. In addition, ablation of LAL activity results in profound NAFLD. Based on this, we predicted that overexpressing LIPA in the livers of mice fed a Western diet (FPC) would prevent the development of NAFLD. As expected, mice fed the FPC diet exhibited numerous markers of NAFLD including hepatomegaly, lipid accumulation, and inflammation. Unexpectedly, LAL overexpression did not attenuate steatosis and had only minor effects on neutral lipid composition. However, LAL overexpression exacerbated inflammatory gene expression and infiltration of immune cells in mice fed the FPC diet. LAL overexpression also resulted in abnormal phagosome accumulation and lysosomal lipid accumulation depending upon the dietary treatment. Hepatic overexpression of LAL drove immune cell infiltration and inflammation and did not attenuate the development of NAFLD suggesting that targeting LAL expression is not a viable route to treat NAFLD.

overall_design: 18 samples were analyzed. 6 from each of the following groups: GFP expressing mice fed a control diet, GFP expressing mice fed the FPC diet, and LIPA expressing mice fed the FPC diet.

first: Michael

last: Lopresti

first: Wenqi

last: Cui

first: Breann

last: Abernathy

first: Gavin

last: Fredrickson

first: Fanta

last: Barrow

first: Arnav

last: Desai

first: Xavier

last: Revelo


title: Cardiac-derived TGF-b1 confers resistance to diet-induced obesity through regulation of adipocyte size and function.

city: Columbus

first: Federica

last: Accornero

state: OH

address: 473 W 12th Ave.

institute: Ohio State University Medical Center

summary: Regulation of organismal homeostasis in response to nutrient availability is a vital physiological process that involves inter-organ communication. Understanding the mechanisms controlling systemic cross talk for maintenance of metabolic health is critical to counteract diet-induced obesity. Here, we show that cardiac-derived transforming growth factor beta 1 (TGF-b1) protects against weight gain and glucose intolerance in mice subjected to high-fat diet. Secretion of TGF-b1 by cardiomyocytes correlates with bioavailability of this factor in circulation. TGF-b1 prevents adipose tissue inflammation independent of body weight and glucose metabolism phenotypes, suggesting protection from adipocyte dysfunction-driven immune cell recruitment. TGF-b1 alters gene expression programs in white adipocytes, favoring their thermogenic fate and consequently increasing their mitochondrial oxygen consumption rates. Ultimately, subcutaneous and visceral white adipose tissue from heart-specific TGF-b1 transgenic mice fail to undergo cellular hypertrophy, leading to reduced overall adiposity during high-fat feeding. Thus, TGF-b1 is a critical mediator of heart-fat communication for regulation of systemic metabolism.

overall_design: A total of four experimental groups with an n =3 were used as input for RNA-seq. The groups are wildtype and heart-specific over-expression of TGFbeta with either control or high fat diet treatment.

first: Jacob

middle: Z

last: Longenecker

first: Scott

middle: A

last: Hinger


title: Foxf1-specific differential gene expression in collagen I-positive murine mesenchymal cells.

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Type I Collagen and Foxf1 expressing double transgenic mice that were labeled for green flourescent protein (GFP) and tdTomato reporters, respectively, were used to sort out three populations. We found that mesenchymal populations which expressed both type I collagen and Foxf1 also expressed high levels of Gli and this population carried a Col14a1 fibroblast signature while the type I collagen expressing MCs that did not express Foxf1 expressed high levels of integrin alpha 8 and carried a Col13a1 fibroblast signature.

overall_design: Three different subsets were sorted such that cell populations expressed both type 1 collagen and Foxf1 (DBL), or only type 1 collagen(ColGFP), or only Foxf1 (TDOnly). RNA was isolated from cell population subsets and submitted to the UM DNA Sequencing Core where ribogone ribosomal RNA depletion was performed prior to RNA-Seq analysis. Bioinformatic analyses was provided by the University of Michigan Bioinformatics Core in the form of differential expression at gene and isoform level, GO annotation of differentially expressed genes, functional enrichment analysis of set of differentially expressed genes and diagnostic plots.

first: Vibha

middle: N

last: Lama


title: Mitochondrial dysfunction governs immunometabolism in leukocytes of patients with acute-on-chronic liver failure

city: Barcelona

first: Ferran

last: Aguilar

state: Barcelona

address: Travessera de Gràcia, 11

country: Spain

institute: EF-CLIF

summary: Background&aims: Patients with acute decompensation (AD) of cirrhosis progressing to acute-on-chronic liver failure (ACLF) present a systemic hyperinflammatory response associated with increased circulating levels of small-molecule metabolites. To investigate whether these alterations reflect inadequate cell energy output, we assessed mitochondrial morphology and central metabolic pathways with emphasis on the tricarboxylic acid (TCA) cycle in peripheral leukocytes from AD patients with and without ACLF. Methods: The study included samples from AD patients (102 without and 126 with ACLF) along with 41 healthy subjects. Leukocyte mitochondria ultrastructure was visualized by transmission electron microscopy and cytosolic and mitochondrial metabolic fluxes were determined by assessing NADH/FADH 2 production from various substrates. Plasma GDF15 and FGF21 were determined by Luminex and acylcarnitines by LC-MS/MS. Gene expression was analyzed by RNA-seq and PCR-based glucose metabolism profiler array. Results: Mitochondrial ultrastructure in patients with advanced cirrhosis was distinguished by cristae rarefication and swelling. The number of mitochondria per leukocyte was higher in patients, accompanied by a reduction in their size. Increased FGF21 and C:6- and C:8-carnitines predicted mortality whereas GDF15 strongly correlated with a gene set signature related to leukocyte activation. Metabolic flux analyses revealed increased energy production in mononuclear leukocytes from patients with preferential involvement of extra-mitochondrial pathways, supported by upregulated expression of genes encoding enzymes of the glycolytic and pentose phosphate pathways. In ACLF patients, mitochondrial function analysis uncovered two break-points in the TCA cycle at the isocitrate dehydrogenase and succinate dehydrogenase level, which were bridged by anaplerotic reactions involving glutaminolysis and nucleoside metabolism. Conclusions: Our findings provide evidence at the cellular, organelle and biochemical levels that severe mitochondrial dysfunction governs immunometabolism in leukocytes from patients with AD cirrhosis and ACLF.

overall_design: RNA-seq transcriptomics in ACLF(n=8), AD(n=5) and Healthy volunteers (n=5)

first: I

last: Zhang

first: A

last: Curto

first: J

last: Clària


title: Identification of JMJD1A and JMJD2B target genes in hypoxic colon carcinoma cells

city: chengdu

first: Lei

last: Qiu

state: sichuan

address: No. 17, Section 3, Renmin South Road

department: Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, and Cancer Center, West China Hospital

institute: sichuan university

summary:
The Hypoxia-Inducible Factors induce the expression of the histone demethylases JMJD1A (KDM3A) and JMJD2B (KDM4B), linking the hypoxic tumor microenvironment to epigenetic mechanisms that may foster tumor progression.
This dataset includes expression data obtained from exposing colon carcinoma cells to hypoxia in combination with siRNA-mediated knockdown of the hypoxia-inducible histone demethylases JMJD1A and JMJD2B.

overall_design:
18 samples were analyzed. The log2-transformed normalized signal intensities were used for downstream pairwise comparisons (using Partek Genomic Suite):
SiControl-Normoxia>SiJMJD1A-Normoxia;
SiJMJD1A-Normoxia>SiControl-Normoxia;
SiControl-Normoxia>SiJMJD2B-Normoxia;
SiJMJD2B-Normoxia>SiControl-Normoxia;
SiControl-Hypoxia>SiControl-Normoxia;
SiControl-Normoxia>SiControl-Hypoxia;
SiControl-Hypoxia>SiJMJD1A-Hypoxia;
SiJMJD1A-Hypoxia>SiControl-Hypoxia;
SiControl-Hypoxia>SiJMJD2B-Hypoxia;
SiJMJD2B-Hypoxia>SiControl-Hypoxia.

first: Adam

last: Krieg